Saturday, 17 November 2012

I have just recently discovered Ipython notebooks[1] they are fantastics and like R sweave[2] they are essential for Reproducible Research.

I use Perl and pdl for bioinformatics research. Being pdl a scientific tool these kind of reproducible research utilities seems a perfect match.

Some time ago in the bio(perl|python) communities they started to look to use a similar approach to sweave but I have not seen much progress on that. A cheap alternative (if your OS is called emacs ;-)) is to use org-mode babel[3]. I like to use babel because I almost always work under ssh connection to my servers using also screen session with emacs -nw . Babel could be a substitute for sweave, but Ipython notebook is a more advanced and interactive beast. You can see this fantastic presentation from Fernando Pérez about scientific Python[4] where he demonstrates its powers.

I don't know yet any Perl tool similar for Ipython notebooks but if it exist I would like to find and use it.

Thanks V, I use PDL with perldl from time to time, but what I was looking for was not the interactive part but the 'notebook' part. The point here is documenting my pipelines and write reproducible examples, like the vignettes/Sweave in R.

Hi sorry to ask such a beginner question here but anyone got to install iperl? I'm fighting with Ubuntu as always. I did what it said in the link https://github.com/EntropyOrg/p5-Devel-IPerl but it doesn't work. I have my ipython notebooks installed inside of Anaconda2. Anyone knows if this approach to install it is compatible with that location?

Thank you for whatever information or link with more clues to solve it.